Bond atom missing in image check (src/domain.cpp:799) and Bond atoms 5903 5904 missing on proc 0 at step 169250 (src/ntopo_bond_all.cpp:61)

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1

Hi,
I have a couple of questions:

Quesn 1: how can I sort atom ids for a data file obtained from the write_data option ?

Quesn 2a: I am simulating a polymer film layer on a substrate. I’ve anchored the substrate using the command “fix 1 all nvt temp 1.0 1.0 1.0 fix 2 all momentum 100 linear 1 1 1”, and set the boundary conditions to prevent interaction between the lower walls of the substrate and the polymers along the z-direction using "boundary p p f "

However, after running the script on my desktop for several steps, it terminated with the following output at step 169000 with an error message:

169000 1.1025765 -8.789107 1.653719 -7.135388 -0.61195637 2.0501892 2.0035002 2.552814 6.6065035
ERROR on proc 0: Bond atoms 5903 5904 missing on proc 0 at step 169250 (src/ntopo_bond_all.cpp:61)
Last command: run 2000000

Quesn 2b: Also, the same scripts when I’m running on cluster terminate before minimization. (attached job error.out)

Setting up cg style minimization …
Unit style : lj
Current step : 0
ERROR on proc 6: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 14: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 22: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 46: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 54: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 70: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 38: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 78: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000
ERROR on proc 86: Bond atom missing in image check (src/domain.cpp:799)
Last command: minimize 0.0 1.0e-8 1000 100000

What could be the reason for this error?

Thanks in advance
T P

2

LAMMPS cannot do this and it makes no sense for LAMMPS for the purposes that data files are used for. Of course you can always write a script or program for yourself that sorts the lines in the Atoms section to your personal delight.

This is difficult to say without seeing the data file, but most likely you have defined one or more bonds with atoms that very far apart and now are moving too fast because of the very high force resulting from that.

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